comparison macros.xml @ 8:843e008b15fd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

7:367ba501b6eb

<macros>
  <token name="@TOOL_VERSION@">1.9</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
      <requirement type="package" version="1.9">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.9">samtools</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

  </token>
  <token name="@INPUT_LIST_FILE@">
$vcfs_list_file
  </token>

  <xml name="macro_fasta_ref">
    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
  </xml>
  <token name="@PREPARE_FASTA_REF@">
<![CDATA[
#set $input_fa_ref = None
#if 'fasta_ref' in $section and $section.fasta_ref:
  #set $input_fa_ref = 'ref.fa'
  ln -s '$section.fasta_ref' $input_fa_ref &&
  samtools faidx $input_fa_ref &&
#end if
]]>
  </token>
  <token name="@FASTA_REF@">
#if $input_fa_ref is not None:
  --fasta-ref $input_fa_ref
#elif 'fasta_ref' in $section and $section.fasta_ref:
  --fasta-ref '${section.fasta_ref}'
#end if
  </token>

  <xml name="macro_ref_fasta">
    <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
         <option value="cached">Locally cached</option>
         <option value="history">History</option>
       </param>
       <when value="cached">
         <param name="ref_file" type="select" label="Select reference genome">
           <options from_data_table="fasta_indexes">
             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
           </options>
           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
         </param>
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
  </xml>


  <xml name="macro_AF_file">
    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
  </xml>
  <!-- This may need to bgzip and tabix the file -->

          <when input="output_type" value="v" format="vcf" />
        </change_format>
      </data>
  </xml>

  <xml name="macro_regions">
    <conditional name="regions">
        <param name="regions_src" type="select" label="Regions">
            <option value="__none__">None</option>
            <option value="regions">regions</option>
            <option value="regions_file">regions-file</option>
        </param>
        <when value="__none__"/>
        <when value="regions">
            <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
                   help="Each region is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
        </when>
        <when value="regions_file">
            <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
        </when>
    </conditional>
  </xml>
  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[
#set $regions_path = None
#if 'regions' in $section
  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:

    #end if
  #end if
#end if
]]>
  </token>
  <token name="@REGIONS@">
#if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
  --regions '$section.regions.regions'
#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
  #if $regions_path is not None:
    --regions-file '$regions_path'
  #else:
    --regions-file '$section.regions.regions_file'
  #end if
#end if
  </token>
  <xml name="macro_targets_file">
            <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
              <yield/>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
  </xml>
  <token name="@PREPARE_TARGETS_FILE@">
<![CDATA[
#set $targets_path = None
#if 'targets' in $section
  #if $section.targets.targets_src == 'targets_file':

  bgzip -c "$section.targets_file" > $targets_path &&
  tabix -s 1 -b 2 -e 2 $targets_path &&
#end if
]]>
  </token>
  <token name="@TARGETS_FILE@">
<![CDATA[
#if $targets_path is not None:
  --targets-file "${section.invert_targets_file}${targets_path}"
#elif $section.targets_file:
  --targets-file "${section.invert_targets_file}${section.targets_file}"
#end if
]]>
  </token>

  <xml name="macro_targets">
    <conditional name="targets">
        <param name="targets_src" type="select" label="Targets">
            <option value="__none__">None</option>
            <option value="targets">targets</option>
            <option value="targets_file">targets-file</option>
        </param>
        <when value="__none__"/>
        <when value="targets">
            <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
                   help="Each target is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
        </when>
        <when value="targets_file">
            <expand macro="macro_targets_file">
            </expand>
        </when>
    </conditional>
  </xml>
  <token name="@TARGETS@">
<![CDATA[
#if $targets_path:
  --targets-file "${section.targets.invert_targets_file}${targets_path}"
#else:
  #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
    --targets '${section.targets.invert_targets_file}${section.targets.targets}'
  #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
    --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
  #end if
#end if
]]>
  </token>

  <xml name="macro_samples">

8:843e008b15fd

<macros>
  <token name="@TOOL_VERSION@">1.9</token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
      <requirement type="package" version="1.9">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.9">samtools</requirement>
  </xml>
  <xml name="matplotlib_requirement">
      <requirement type="package" version="3.1.0">matplotlib</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

  </token>
  <token name="@INPUT_LIST_FILE@">
$vcfs_list_file
  </token>

  <xml name="test_using_reference" token_select_from="history" token_ref="">
    <conditional name="reference_source">
        <param name="reference_source_selector" value="@SELECT_FROM@" />
        <param name="fasta_ref" ftype="fasta" value="@REF@" />
    </conditional>
  </xml>

  <xml name="macro_fasta_ref">
    <conditional name="reference_source">
        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="cached">Use a built-in genome</option>
            <option value="history">Use a genome from the history</option>
        </param>
        <when value="cached">
            <param name="fasta_ref" type="select" label="Reference genome">
                <options from_data_table="fasta_indexes">
                    <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                </options>
            </param>
        </when>
        <when value="history">
            <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
        </when>
    </conditional>
  </xml>
  <token name="@PREPARE_FASTA_REF@">
<![CDATA[
#set $input_fa_ref = None
#if 'fasta_ref' in $section and $section.fasta_ref:
  #if 'reference_source_selector' in $section:
    #if str($section.reference_source_selector) == "history":
      #set $input_fa_ref = 'ref.fa'
      ln -s '$section.fasta_ref' $input_fa_ref &&
      samtools faidx $input_fa_ref &&
    #else:
      #set $input_fa_ref = str($section.fasta_ref.fields.path)
    #end if
  #end if
#end if
]]>
  </token>
  <token name="@FASTA_REF@">
#if $input_fa_ref is not None:
  --fasta-ref $input_fa_ref
#elif 'fasta_ref' in $section and $section.fasta_ref:
  --fasta-ref '${section.fasta_ref}'
#end if
  </token>

  <xml name="macro_AF_file">
    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
  </xml>
  <!-- This may need to bgzip and tabix the file -->

          <when input="output_type" value="v" format="vcf" />
        </change_format>
      </data>
  </xml>

  <xml name="macro_invert_targets">
    <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
    label="Invert Targets"
    help="inverts the query/filtering applied by the targets" />
  </xml>

  <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
    <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
        <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
            <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
        </param>
        <param name="start" type="text" label="@LABEL_TYPE@ start position">
            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
        </param>
        <param name="stop" type="text" label="@LABEL_TYPE@ end position">
            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
        </param>
        <yield />
    </repeat>
  </xml>

  <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
    <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
  </xml>

  <xml name="macro_restrict" token_type="region" token_label_type="Region" >
    <conditional name="@TYPE@s">
        <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
            <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
            <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
            <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
        </param>
        <when value="__none__"/>
        <when value="@TYPE@s">
            <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
            <yield />
        </when>
        <when value="@TYPE@s_file">
            <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
            <yield />
        </when>        
    </conditional>
  </xml>

  <token name="@PARSE_INTERVALS@">
<![CDATA[
#set $components = []
#for $i in $intervals:
  #set $chrom = str($i.chrom).strip()
  #set $start = str($i.start).strip()
  #set $stop = str($i.stop).strip()
  #if $start or $stop:
    $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)
]]>
  </token>
  
  <token name="@REGIONS@">
<![CDATA[
#if $section.regions.regions_src == 'regions':
  #set $intervals = $section.regions.regions
  @PARSE_INTERVALS@
  --regions '$intervals_spec'
#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
  #if $regions_path is not None:
    --regions-file '$regions_path'
  #else:
    --regions-file '$section.regions.regions_file'
  #end if
#end if
]]>
  </token>
  
  <token name="@TARGETS@">
<![CDATA[
#if $targets_path:
  --targets-file "${section.targets.invert_targets_file}${targets_path}"
#elif $section.targets.targets_src == 'targets':
  #set $intervals = $section.targets.targets
  @PARSE_INTERVALS@
  --targets '${section.targets.invert_targets_file}$intervals_spec'
#elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
  --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
#end if
]]>
  </token>

  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[
#set $regions_path = None
#if 'regions' in $section
  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:

    #end if
  #end if
#end if
]]>
  </token>

  <token name="@PREPARE_TARGETS_FILE@">
<![CDATA[
#set $targets_path = None
#if 'targets' in $section
  #if $section.targets.targets_src == 'targets_file':

  bgzip -c "$section.targets_file" > $targets_path &&
  tabix -s 1 -b 2 -e 2 $targets_path &&
#end if
]]>
  </token>

  <token name="@TARGETS_FILE@">
<![CDATA[
#if $targets_path is not None:
  --targets-file "${section.invert_targets_file}${targets_path}"
#elif $section.targets_file:
  --targets-file "${section.invert_targets_file}${section.targets_file}"
#end if
]]>
  </token>

  <xml name="macro_samples">